Re: [R] help with cube3d cube size
Duncan & Ben, Thanks for giving me some tips as to how I can best investigate packages. I"ve been using ESS-Emacs and the help pages are HTML. Looks like I need to figure out how to enable HTML help. As for a draft vignette, sure, I would be happy (and honored) to contribute as best I can. I would need a lot of help from the two of you, but it would be a good learning experience for me and give me a chance to give something back to the community which has been so good to me. Speaking of vignettes, I wonder if there should be a vignette written called "navigating new functions and packages for the R beginner" or be included as a chapter in "An Introduction to R", which focuses on R-base functionality. I"m just musing here, but I often think that if I need to learn something perhaps others do too. One thing at a time, however, so I'll work on a draft and send it to you for comments and input. Ben, if you get such a list of packages with functions that depend on rgl, send it to me. Mark On Thu, Jun 26, 2008 at 7:02 AM, Duncan Murdoch <[EMAIL PROTECTED]> wrote: > Mark Kimpel wrote: >> >> Thanks for the pointers. I think the package is great, just want to >> use it to its full potential without driving the list crazy with >> questions. Below is my output to help and sessionInfo(). I don't see >> the scaling functions, although I now see that they can be retrieved >> with ?matrices. You guys are the experts as to what should go where, >> but for someone unfamiliar with how rgl works, having them print out >> with help(package = "rgl") would make some of these functions more >> obvious to the newbie. Mark >> > > The issue here is that several of those are documented on the same page, and > that index lists the names of help pages, not all of the aliases that point > there. The index in the HTML help version (or the CHM help in Windows) > repeats each alias, so you'll see things like > > scale3dWork with homogeneous coordinates > scaleMatrixWork with homogeneous coordinates > > as well as the entry for matrices as below. I can see arguments for both: > repetition is bad, full coverage is good. The index in the pdf document is > another approach: it lists all the aliases, and tells you which topic > documents them. > > All of this is common to all R packages; rgl isn't doing anything special to > produce these lists. > > Duncan Murdoch >> >> aspect3dSet the aspect ratios of the current plot >> axes3d Draw boxes, axes and other text outside the >>data >> ellipse3d Make an ellipsoid >> grid3d Add a grid to a 3D plot >> matricesWork with homogeneous coordinates >> par3d Set or Query RGL Parameters >> par3dinterp Interpolator for par3d parameters >> persp3d Surface plots >> play3d Play animation of rgl scene >> plot3d 3D Scatterplot >> points3dadd primitive set shape >> qmesh3d 3D Quadrangle Mesh objects >> r3d Generic 3D interface >> rgl-package 3D visualization device system >> rgl.bboxSet up Bounding Box decoration >> rgl.bg Set up Background >> rgl.bringtotop Assign focus to an RGL window >> rgl.clear scene management >> rgl.light add light source >> rgl.materialGeneric Appearance setup >> rgl.postscript export screenshot >> rgl.primitive add primitive set shape >> rgl.setMouseCallbacks User callbacks on mouse events >> rgl.snapshotexport screenshot >> rgl.spheres add sphere set shape >> rgl.surface add height-field surface shape >> rgl.texts add text >> rgl.user2window Convert between rgl user and window coordinates >> rgl.viewpoint Set up viewpoint >> select3dSelect a rectangle in an RGL scene >> spin3d Create a function to spin a scene at a fixed >>rate >> sprites3d add sprite set shape >> subdivision3d generic subdivision surface method >> surface3d add height-field surface shape >> >> >> >>> >>> sessionInfo() >>> >> >> R version 2.7.1 (2008-06-23) >> i686-pc-linux-gnu >> >> locale: >> >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] rgl_0.79 graph_1.18.1 >> >> loaded via a namespace (and not attached): >> [1] cluster_1.11.11 tools_2.7.1 >> >> On Wed, Jun 25, 2008 at 5:25 PM, Duncan Murdoch <[EMAIL PROTECTED]> >> wrote: >> >>> >>> Mark Kimpel wrote: >>> Ben and Du
Re: [R] help with cube3d cube size
One way to get at all the functions (although not as easy as help() is library(rgl); ls(pos=2) which literally lists the available functions. As Duncan said, there are multiple functions documented in each page and only the page definitions show up (e.g. "matrices" is the page for "work[ing] with homogeneous coordinates", and contains 10 different functions ...) or ? because some functions are hidden in the namespace [but I think the former]). (2) demo(package="rgl") may be helpful (3) it would be interesting to try to extract a list of all the package that have rgl as dependencies or suggestions -- I know offhand of emdbook, Rcmdr, vegan ... (4) would you like to draft a vignette as you figure rgl out? Ben Bolker Mark Kimpel wrote: Ben and Duncan, Thanks for your helpful suggestions. I"m having some difficulty navigating this really good package using my normal learning techniques. When I do 'help(package = "rgl") it seems only a very small subset of functions available show up. Perusing the rgl.pdf downloaded from CRAN demonstrates the same lack of documentation. There is no vignette. In addition, I have found at least one other package with 3d functions (emdbook::curve3d()). What is the best resource for learning about all the foo3d() and lower level functionality that rgl and its dependents provide? I saw a book at B&N just last week on openGL. Would that be helpful? Mark On Tue, Jun 24, 2008 at 10:54 PM, Ben Bolker <[EMAIL PROTECTED]> wrote: Mark Kimpel gmail.com> writes: I'm using the command below on an open3d() object to create a shaded cube. Changes to myScalingFactor do not effect changes in the size of the cube. What is the correct approach? Mark how about scale3d() ? shade3d(translate3d(scale3d(cube3d(),5,5,5),-6,1,-1),col="blue", alpha = 0.2) shade3d(translate3d(cube3d(),-6,1,-1),col="green", alpha = 0.2) shade3d(translate3d(scale3d(cube3d(),10,10,10),-6,1,-1),col="red", alpha = 0.2) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help with cube3d cube size
Mark Kimpel wrote: Thanks for the pointers. I think the package is great, just want to use it to its full potential without driving the list crazy with questions. Below is my output to help and sessionInfo(). I don't see the scaling functions, although I now see that they can be retrieved with ?matrices. You guys are the experts as to what should go where, but for someone unfamiliar with how rgl works, having them print out with help(package = "rgl") would make some of these functions more obvious to the newbie. Mark The issue here is that several of those are documented on the same page, and that index lists the names of help pages, not all of the aliases that point there. The index in the HTML help version (or the CHM help in Windows) repeats each alias, so you'll see things like scale3dWork with homogeneous coordinates scaleMatrixWork with homogeneous coordinates as well as the entry for matrices as below. I can see arguments for both: repetition is bad, full coverage is good. The index in the pdf document is another approach: it lists all the aliases, and tells you which topic documents them. All of this is common to all R packages; rgl isn't doing anything special to produce these lists. Duncan Murdoch aspect3dSet the aspect ratios of the current plot axes3d Draw boxes, axes and other text outside the data ellipse3d Make an ellipsoid grid3d Add a grid to a 3D plot matricesWork with homogeneous coordinates par3d Set or Query RGL Parameters par3dinterp Interpolator for par3d parameters persp3d Surface plots play3d Play animation of rgl scene plot3d 3D Scatterplot points3dadd primitive set shape qmesh3d 3D Quadrangle Mesh objects r3d Generic 3D interface rgl-package 3D visualization device system rgl.bboxSet up Bounding Box decoration rgl.bg Set up Background rgl.bringtotop Assign focus to an RGL window rgl.clear scene management rgl.light add light source rgl.materialGeneric Appearance setup rgl.postscript export screenshot rgl.primitive add primitive set shape rgl.setMouseCallbacks User callbacks on mouse events rgl.snapshotexport screenshot rgl.spheres add sphere set shape rgl.surface add height-field surface shape rgl.texts add text rgl.user2window Convert between rgl user and window coordinates rgl.viewpoint Set up viewpoint select3dSelect a rectangle in an RGL scene spin3d Create a function to spin a scene at a fixed rate sprites3d add sprite set shape subdivision3d generic subdivision surface method surface3d add height-field surface shape sessionInfo() R version 2.7.1 (2008-06-23) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rgl_0.79 graph_1.18.1 loaded via a namespace (and not attached): [1] cluster_1.11.11 tools_2.7.1 On Wed, Jun 25, 2008 at 5:25 PM, Duncan Murdoch <[EMAIL PROTECTED]> wrote: Mark Kimpel wrote: Ben and Duncan, Thanks for your helpful suggestions. I"m having some difficulty navigating this really good package using my normal learning techniques. When I do 'help(package = "rgl") it seems only a very small subset of functions available show up. I think the full list shows up there, if you're using a current version. What specific function is missing? Perusing the rgl.pdf downloaded from CRAN demonstrates the same lack of documentation. All of the functions intended for users are documented, and they show up in rgl.pdf. There is no vignette. In addition, I have found at least one other package with 3d functions (emdbook::curve3d()). A vignette would be nice, but there isn't one. Our paper from useR 2007 is the most recent reference (see http://www.r-project.org/conferences/useR-2007/program/presentations/murdoch.pdf); it cites Daniel's 2003 thesis and the 2003 paper about the package. After those, the NEWS file lists some recent additions. emdbook makes use of rgl and some other 3d engines, as does misc3d. scatterplot3d does it's own drawing. rggobi is a completely different interactive package. What is the best resource for learning about all the foo3d() and lower level functionality that rgl and its dependents provide? I saw a book at B&N jus
Re: [R] help with cube3d cube size
Thanks for the pointers. I think the package is great, just want to use it to its full potential without driving the list crazy with questions. Below is my output to help and sessionInfo(). I don't see the scaling functions, although I now see that they can be retrieved with ?matrices. You guys are the experts as to what should go where, but for someone unfamiliar with how rgl works, having them print out with help(package = "rgl") would make some of these functions more obvious to the newbie. Mark aspect3dSet the aspect ratios of the current plot axes3d Draw boxes, axes and other text outside the data ellipse3d Make an ellipsoid grid3d Add a grid to a 3D plot matricesWork with homogeneous coordinates par3d Set or Query RGL Parameters par3dinterp Interpolator for par3d parameters persp3d Surface plots play3d Play animation of rgl scene plot3d 3D Scatterplot points3dadd primitive set shape qmesh3d 3D Quadrangle Mesh objects r3d Generic 3D interface rgl-package 3D visualization device system rgl.bboxSet up Bounding Box decoration rgl.bg Set up Background rgl.bringtotop Assign focus to an RGL window rgl.clear scene management rgl.light add light source rgl.materialGeneric Appearance setup rgl.postscript export screenshot rgl.primitive add primitive set shape rgl.setMouseCallbacks User callbacks on mouse events rgl.snapshotexport screenshot rgl.spheres add sphere set shape rgl.surface add height-field surface shape rgl.texts add text rgl.user2window Convert between rgl user and window coordinates rgl.viewpoint Set up viewpoint select3dSelect a rectangle in an RGL scene spin3d Create a function to spin a scene at a fixed rate sprites3d add sprite set shape subdivision3d generic subdivision surface method surface3d add height-field surface shape > sessionInfo() R version 2.7.1 (2008-06-23) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rgl_0.79 graph_1.18.1 loaded via a namespace (and not attached): [1] cluster_1.11.11 tools_2.7.1 On Wed, Jun 25, 2008 at 5:25 PM, Duncan Murdoch <[EMAIL PROTECTED]> wrote: > Mark Kimpel wrote: >> >> Ben and Duncan, >> >> Thanks for your helpful suggestions. I"m having some difficulty >> navigating this really good package using my normal learning >> techniques. When I do 'help(package = "rgl") it seems only a very >> small subset of functions available show up. > > I think the full list shows up there, if you're using a current version. > What specific function is missing? >> >> Perusing the rgl.pdf >> downloaded from CRAN demonstrates the same lack of documentation. >> > > All of the functions intended for users are documented, and they show up in > rgl.pdf. >> >> There is no vignette. In addition, I have found at least one other >> package with 3d functions (emdbook::curve3d()). >> > > A vignette would be nice, but there isn't one. Our paper from useR 2007 is > the most recent reference (see > http://www.r-project.org/conferences/useR-2007/program/presentations/murdoch.pdf); > it cites Daniel's 2003 thesis and the 2003 paper about the package. > After those, the NEWS file lists some recent additions. > > emdbook makes use of rgl and some other 3d engines, as does misc3d. > scatterplot3d does it's own drawing. rggobi is a completely different > interactive package. >> >> What is the best resource for learning about all the foo3d() and lower >> level functionality that rgl and its dependents provide? I saw a book >> at B&N just last week on openGL. Would that be helpful? >> > > It might, but probably not. rgl is intended to be a higher level R-style > interface to the things described in a book like that. So if you have a > particular question about how to do something, you'd never find it there. > On the other hand, if you want to know if something is possible, then that > might be a place to look for ideas. > > Duncan Murdoch >> >> Mark >> >> On Tue, Jun 24, 2008 at 10:54 PM, Ben Bolker <[EMAIL PROTECTED]> wrote: >> >>> >>> Mark Kimpel gmail.com> writes: >>> >>> I'm using the command below on an open3d() object to create a shaded cube. Changes to myScalingFactor do not effect changes in the size of the cube. What is
Re: [R] help with cube3d cube size
Mark Kimpel wrote: Ben and Duncan, Thanks for your helpful suggestions. I"m having some difficulty navigating this really good package using my normal learning techniques. When I do 'help(package = "rgl") it seems only a very small subset of functions available show up. I think the full list shows up there, if you're using a current version. What specific function is missing? Perusing the rgl.pdf downloaded from CRAN demonstrates the same lack of documentation. All of the functions intended for users are documented, and they show up in rgl.pdf. There is no vignette. In addition, I have found at least one other package with 3d functions (emdbook::curve3d()). A vignette would be nice, but there isn't one. Our paper from useR 2007 is the most recent reference (see http://www.r-project.org/conferences/useR-2007/program/presentations/murdoch.pdf); it cites Daniel's 2003 thesis and the 2003 paper about the package. After those, the NEWS file lists some recent additions. emdbook makes use of rgl and some other 3d engines, as does misc3d. scatterplot3d does it's own drawing. rggobi is a completely different interactive package. What is the best resource for learning about all the foo3d() and lower level functionality that rgl and its dependents provide? I saw a book at B&N just last week on openGL. Would that be helpful? It might, but probably not. rgl is intended to be a higher level R-style interface to the things described in a book like that. So if you have a particular question about how to do something, you'd never find it there. On the other hand, if you want to know if something is possible, then that might be a place to look for ideas. Duncan Murdoch Mark On Tue, Jun 24, 2008 at 10:54 PM, Ben Bolker <[EMAIL PROTECTED]> wrote: Mark Kimpel gmail.com> writes: I'm using the command below on an open3d() object to create a shaded cube. Changes to myScalingFactor do not effect changes in the size of the cube. What is the correct approach? Mark how about scale3d() ? shade3d(translate3d(scale3d(cube3d(),5,5,5),-6,1,-1),col="blue", alpha = 0.2) shade3d(translate3d(cube3d(),-6,1,-1),col="green", alpha = 0.2) shade3d(translate3d(scale3d(cube3d(),10,10,10),-6,1,-1),col="red", alpha = 0.2) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help with cube3d cube size
Ben and Duncan, Thanks for your helpful suggestions. I"m having some difficulty navigating this really good package using my normal learning techniques. When I do 'help(package = "rgl") it seems only a very small subset of functions available show up. Perusing the rgl.pdf downloaded from CRAN demonstrates the same lack of documentation. There is no vignette. In addition, I have found at least one other package with 3d functions (emdbook::curve3d()). What is the best resource for learning about all the foo3d() and lower level functionality that rgl and its dependents provide? I saw a book at B&N just last week on openGL. Would that be helpful? Mark On Tue, Jun 24, 2008 at 10:54 PM, Ben Bolker <[EMAIL PROTECTED]> wrote: > Mark Kimpel gmail.com> writes: > >> >> I'm using the command below on an open3d() object to create a shaded >> cube. Changes to myScalingFactor do not effect changes in the size of >> the cube. What is the correct approach? Mark > > > > how about scale3d() ? > > shade3d(translate3d(scale3d(cube3d(),5,5,5),-6,1,-1),col="blue", alpha = 0.2) > shade3d(translate3d(cube3d(),-6,1,-1),col="green", alpha = 0.2) > shade3d(translate3d(scale3d(cube3d(),10,10,10),-6,1,-1),col="red", alpha = > 0.2) > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help with cube3d cube size
Mark Kimpel gmail.com> writes: > > I'm using the command below on an open3d() object to create a shaded > cube. Changes to myScalingFactor do not effect changes in the size of > the cube. What is the correct approach? Mark how about scale3d() ? shade3d(translate3d(scale3d(cube3d(),5,5,5),-6,1,-1),col="blue", alpha = 0.2) shade3d(translate3d(cube3d(),-6,1,-1),col="green", alpha = 0.2) shade3d(translate3d(scale3d(cube3d(),10,10,10),-6,1,-1),col="red", alpha = 0.2) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help with cube3d cube size
Mark Kimpel wrote: I'm using the command below on an open3d() object to create a shaded cube. Changes to myScalingFactor do not effect changes in the size of the cube. What is the correct approach? Mark shade3d(translate3d(cube3d(identityMatrix() * myScalingFactor),-6,1,-1),col="green", alpha = 0.2) Homogeneous coordinates are strange. Your identityMatrix() * myScalingFactor produces a matrix that has the same effect as not multiplying. You need scaleMatrix(myScalingFactor, myScalingFactor, myScalingFactor) to get a size change. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
